ArticleProteins2014
Antibody structure determination using a combination of homology modeling, energy-based refinement, and loop prediction.
Article in Proteins, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 122 papers.
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Who cites it
122 citing papers in PubMed.
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- Clinical, Molecular and Bioinformatic Study of Common Thrombophilia Mutation Factor V Leiden.Advances in experimental medicine and biology · 2026Article
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- RiSKs in Computational Modeling of Isoform-Selective RSK Inhibitors.Journal of chemical information and modeling · 2025Review
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- A potent nonapeptide inhibitor for the CXCL12/HMGB1 heterocomplex: A computational and experimental approach.Computational and structural biotechnology journal · 2025Article
- Prediction of SafD adhesin strong binding peptides for pilus proteins assembly suppression in the prevention ofIn silico pharmacology · 2025Article
- Discovering Active Chemotherapeutic Agents for Sexually Transmitted Diseases to Inhibit Pathogenic HPV-16-E6 Protein.Current drug discovery technologies · 2025Article
- Development of a potential vaccine against Capripox virus implementing reverse vaccinology and pan-genomic immunoinformatics.PloS one · 2025Article
62 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
Funding
Abstract
We present the blinded prediction results in the Second Antibody Modeling Assessment (AMA-II) using a fully automatic antibody structure prediction method implemented in the programs BioLuminate and Prime. We have developed a novel knowledge based approach to model the CDR loops, using a combination of sequence similarity, geometry matching, and the clustering of database structures. The homology models are further optimized with a physics-based energy function (VSGB2.0), which improves the model quality significantly. H3 loop modeling remains the most challenging task. Our ab initio loop prediction performs well for the H3 loop in the crystal structure context, and allows improved results when refining the H3 loops in the context of homology models. For the 10 human and mouse derived antibodies in this assessment, the average RMSDs for the homology model Fv and framework regions are 1.19 Å and 0.74 Å, respectively. The average RMSDs for five non-H3 CDR loops range from 0.61 Å to 1.05 Å, and the H3 loop average RMSD is 2.91 Å using our knowledge-based loop prediction approach. The ab initio H3 loop predictions yield an average RMSD of 1.28 Å when performed in the context of the crystal structure and 2.67 Å in the context of the homology modeled structure. Notably, our method for predicting the H3 loop in the crystal structure environment ranked first among the seven participating groups in AMA-II, and our method made the best prediction among all participants for seven of the ten targets.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.